Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. lmbwide.login complete /public/xtal/CCP4/ccp4-64/Prerelease ccp4_base /public/xtal lmbbase +------------------------------------------------ LMB crystallography software CCP4 release 7.1 installed 23/04/2020 (DB) Type "ccp4i2" to get the new improved interface for new projects NOW IMPROVED WITH ACCESS TO ccp4i1 projects **** If you really want to use the older (7.0) version, edit your .login to "source /public/xtal/ccp4/xtal-7.0.login" and login again ------------------------------------------------------------------------------ phenix release 1.18 (3874) 20 5 20 (JL) "phenix &" for GUI ------------------------------------------------------------------------------ sharp server is on hal:8081, Sharp version 2.9.0 7/2/20 (DB) ------------------------------------------------------------------------------ XDS 4/2020 (DB), generate_XDS.INP / eiger_XDS.INP 5/2019 (JL) ------------------------------------------------------------------------------ MAIN 2019 JL 3/2019 ------------------------------------------------------------------------------ iMosflm will now read "master" hdf5 files, including the Eiger2 detector at DLS AGWL 5/2019 ------------------------------------------------------------------------------ Buster and autoPROC update 19/3/20 (DB) ------------------------------------------------------------------------------ MoRDa database updated to version 31 13/04/2020 (DB/JL) ------------------------------------------------------------------------------ ************************************************** MRC image processing programs have moved. You are using image2010 by default. If you wish to use the frozen image2000 you need to : source /public/EM/image2000/com/image.login and source /public/EM/image2000/com/image.cshrc Jude Short (F46 x2039 jms@mrc-lmb.cam.ac.uk) 09.03.2011 ************************************************** Path to mpiexec: /public/EM/OpenMPI/openmpi-2.0.1/build/bin/mpiexec Path to relion_refine_mpi: /lmb/home/tnakane/prog/relion-devel-lmb/build-test/bin/relion_refine_mpi Libraries for relion_refine_mpi: linux-vdso.so.1 => (0x00007ffddbfde000) libcufft.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcufft.so.9.0 (0x00002b3a2cdb3000) libmpi.so.20 => /public/EM/OpenMPI/openmpi-2.0.1/build/lib/libmpi.so.20 (0x00002b3a34e54000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b3a35133000) libtiff.so.5 => /lib64/libtiff.so.5 (0x00002b3a35337000) libfftw3.so.3 => /lmb/home/tnakane/prog/relion-devel-lmb/external/fftw/lib/libfftw3.so.3 (0x00002b3a355ab000) libfftw3f.so.3 => /lmb/home/tnakane/prog/relion-devel-lmb/external/fftw/lib/libfftw3f.so.3 (0x00002b3a3592a000) libcurand.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcurand.so.9.0 (0x00002b3a35d35000) libpng15.so.15 => /lib64/libpng15.so.15 (0x00002b3a39c99000) libcudart.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcudart.so.9.0 (0x00002b3a39ec4000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00002b3a3a131000) libm.so.6 => /lib64/libm.so.6 (0x00002b3a3a439000) libgomp.so.1 => /lib64/libgomp.so.1 (0x00002b3a3a73b000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b3a3a961000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b3a3ab77000) libc.so.6 => /lib64/libc.so.6 (0x00002b3a3ad93000) librt.so.1 => /lib64/librt.so.1 (0x00002b3a3b160000) libopen-rte.so.20 => /net/nfs1/public/EM/OpenMPI/openmpi-2.0.1/build/lib/libopen-rte.so.20 (0x00002b3a3b368000) libopen-pal.so.20 => /net/nfs1/public/EM/OpenMPI/openmpi-2.0.1/build/lib/libopen-pal.so.20 (0x00002b3a3b5e7000) libutil.so.1 => /lib64/libutil.so.1 (0x00002b3a3b8cd000) /lib64/ld-linux-x86-64.so.2 (0x00002b3a2cb8f000) libjbig.so.2.0 => /lib64/libjbig.so.2.0 (0x00002b3a3bad0000) libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00002b3a3bcdc000) libz.so.1 => /lib64/libz.so.1 (0x00002b3a3bf31000) RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE = /public/EM/SIDESPLITTER/sidesplitter_wrapper.sh SIDESPLITTER = /public/EM/SIDESPLITTER/sidesplitter RUN STARTED AT 1593217330 ----------------------------------------------------------- Reading in optimiser.star ... + Reading in mask ... + The subtracted particles will be re-centred on projections of 3D-coordinate: (14.3241 , -56.4481 , 16.9611) + Calculating Fourier transforms of the maps ... + Subtracting all particles ... 000/??? sec ~~(,_,"> [oo] 0.01/1.57 hrs ~~(,_,"> 0.02/1.45 hrs ~~(,_,"> 0.04/1.47 hrs .~~(,_,"> 0.05/1.51 hrs .~~(,_,"> 0.06/1.51 hrs ..~~(,_,"> 0.07/1.46 hrs ..~~(,_,"> 0.08/1.44 hrs ...~~(,_,"> 0.09/1.42 hrs ...~~(,_,"> 0.11/1.43 hrs ....~~(,_,"> 0.12/1.42 hrs ....~~(,_,"> 0.13/1.43 hrs .....~~(,_,"> 0.14/1.43 hrs .....~~(,_,"> 0.15/1.42 hrs ......~~(,_,"> 0.17/1.42 hrs ......~~(,_,"> 0.18/1.43 hrs .......~~(,_,"> 0.19/1.42 hrs .......~~(,_,"> 0.20/1.43 hrs ........~~(,_,"> 0.21/1.43 hrs ........~~(,_,"> 0.23/1.43 hrs .........~~(,_,"> 0.24/1.44 hrs .........~~(,_,"> 0.25/1.44 hrs ..........~~(,_,"> 0.27/1.45 hrs ..........~~(,_,"> 0.28/1.45 hrs ...........~~(,_,"> 0.29/1.45 hrs ...........~~(,_,"> 0.30/1.44 hrs ............~~(,_,"> 0.31/1.44 hrs ............~~(,_,"> 0.32/1.44 hrs .............~~(,_,"> 0.34/1.45 hrs .............~~(,_,"> 0.35/1.45 hrs ..............~~(,_,"> 0.36/1.44 hrs ..............~~(,_,"> 0.37/1.44 hrs ...............~~(,_,"> 0.38/1.44 hrs ...............~~(,_,"> 0.39/1.43 hrs ................~~(,_,"> 0.40/1.43 hrs ................~~(,_,"> 0.41/1.42 hrs .................~~(,_,"> 0.43/1.42 hrs .................~~(,_,"> 0.44/1.43 hrs ..................~~(,_,"> 0.45/1.42 hrs ..................~~(,_,"> 0.46/1.41 hrs ...................~~(,_,"> 0.47/1.41 hrs ...................~~(,_,"> 0.48/1.40 hrs ....................~~(,_,"> 0.49/1.40 hrs ....................~~(,_,"> 0.50/1.39 hrs .....................~~(,_,"> 0.51/1.39 hrs .....................~~(,_,"> 0.52/1.38 hrs ......................~~(,_,"> 0.53/1.38 hrs ......................~~(,_,"> 0.54/1.37 hrs .......................~~(,_,"> 0.55/1.37 hrs .......................~~(,_,"> 0.55/1.36 hrs ........................~~(,_,"> 0.56/1.35 hrs ........................~~(,_,"> 0.57/1.35 hrs .........................~~(,_,"> 0.58/1.34 hrs .........................~~(,_,"> 0.59/1.33 hrs ..........................~~(,_,"> 0.60/1.32 hrs ..........................~~(,_,"> 0.60/1.32 hrs ...........................~~(,_,"> 0.61/1.31 hrs ...........................~~(,_,"> 0.62/1.31 hrs ............................~~(,_,"> 0.63/1.30 hrs ............................~~(,_,"> 0.64/1.30 hrs .............................~~(,_,"> 0.65/1.30 hrs .............................~~(,_,"> 0.66/1.29 hrs ..............................~~(,_,"> 0.67/1.29 hrs ..............................~~(,_,"> 0.67/1.28 hrs ...............................~~(,_,"> 0.68/1.28 hrs ...............................~~(,_,"> 0.69/1.27 hrs ................................~~(,_,"> 0.70/1.27 hrs ................................~~(,_,"> 0.71/1.26 hrs .................................~~(,_,"> 0.71/1.26 hrs .................................~~(,_,"> 0.72/1.26 hrs ..................................~~(,_,"> 0.73/1.25 hrs ..................................~~(,_,"> 0.74/1.25 hrs ...................................~~(,_,"> 0.75/1.24 hrs ...................................~~(,_,"> 0.76/1.24 hrs ....................................~~(,_,"> 0.77/1.24 hrs ....................................~~(,_,"> 0.77/1.24 hrs .....................................~~(,_,"> 0.78/1.24 hrs .....................................~~(,_,"> 0.79/1.24 hrs ......................................~~(,_,"> 0.80/1.24 hrs ......................................~~(,_,"> 0.81/1.24 hrs .......................................~~(,_,"> 0.82/1.24 hrs .......................................~~(,_,"> 0.83/1.23 hrs ........................................~~(,_,"> 0.84/1.23 hrs ........................................~~(,_,"> 0.85/1.23 hrs .........................................~~(,_,"> 0.86/1.23 hrs .........................................~~(,_,"> 0.87/1.23 hrs ..........................................~~(,_,"> 0.88/1.23 hrs ..........................................~~(,_,"> 0.89/1.23 hrs ...........................................~~(,_,"> 0.90/1.23 hrs ...........................................~~(,_,"> 0.91/1.23 hrs ............................................~~(,_,"> 0.92/1.23 hrs ............................................~~(,_,"> 0.93/1.23 hrs .............................................~~(,_,"> 0.94/1.23 hrs .............................................~~(,_,"> 0.95/1.23 hrs ..............................................~~(,_,"> 0.96/1.22 hrs ..............................................~~(,_,"> 0.97/1.22 hrs ...............................................~~(,_,"> 0.98/1.22 hrs ...............................................~~(,_,"> 0.99/1.22 hrs ................................................~~(,_,"> 1.00/1.22 hrs ................................................~~(,_,"> 1.01/1.22 hrs .................................................~~(,_,"> 1.02/1.22 hrs .................................................~~(,_,"> 1.03/1.22 hrs ..................................................~~(,_,"> 1.04/1.22 hrs ..................................................~~(,_,"> 1.05/1.22 hrs ...................................................~~(,_,"> 1.06/1.22 hrs ...................................................~~(,_,"> 1.07/1.22 hrs ....................................................~~(,_,"> 1.08/1.22 hrs ....................................................~~(,_,"> 1.09/1.22 hrs .....................................................~~(,_,"> 1.10/1.22 hrs .....................................................~~(,_,"> 1.11/1.22 hrs ......................................................~~(,_,"> 1.12/1.22 hrs ......................................................~~(,_,"> 1.13/1.22 hrs .......................................................~~(,_,"> 1.14/1.22 hrs .......................................................~~(,_,"> 1.15/1.22 hrs ........................................................~~(,_,"> 1.16/1.22 hrs ........................................................~~(,_,"> 1.17/1.22 hrs .........................................................~~(,_,"> 1.18/1.22 hrs .........................................................~~(,_,"> 1.19/1.22 hrs ..........................................................~~(,_,"> 1.19/1.22 hrs ..........................................................~~(,_,"> 1.20/1.21 hrs ...........................................................~~(,_,"> 1.21/1.21 hrs ...........................................................~~(,_,"> 1.21/1.21 hrs ............................................................~~(,_,"> + Saved STAR file with 403474 subtracted particles in Subtract/job387/particles_subtracted.star ----------------------------------------------------------- RUN FINISHED AT 1593221773 ELAPSED WALL CLOCK TIME: 4443 Running epilog script on fmb341.lmb.internal Sat 27 Jun 02:36:13 BST 2020 Removing files owned by mwilkin on /ssd Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. lmbwide.login complete /public/xtal/CCP4/ccp4-64/Prerelease ccp4_base /public/xtal lmbbase +------------------------------------------------ LMB crystallography software CCP4 release 7.1 installed 23/04/2020 (DB) updated 05/01/21 (DB) Type "ccp4i2" to get the new improved interface for new projects NOW IMPROVED WITH ACCESS TO ccp4i1 projects **** If you really want to use the older (7.0) version, edit your .login to "source /public/xtal/ccp4/xtal-7.0.login" and login again ------------------------------------------------------------------------------ phenix release 1.19.1 (4122) 1/21 JL "phenix &" for GUI ------------------------------------------------------------------------------ sharp server is on hal:8081, Sharp version 2.9.0 7/2/20 (DB) ------------------------------------------------------------------------------ XDS 01/10/2020 (DB), generate_XDS.INP / eiger_XDS.INP 5/2019 (JL) ------------------------------------------------------------------------------ MAIN 2020 JL 9/20 ------------------------------------------------------------------------------ iMosflm will now read "master" hdf5 files, including the Eiger2 detector at DLS AGWL 5/2019 ------------------------------------------------------------------------------ Buster and autoPROC update 02/10/20 (DB) ------------------------------------------------------------------------------ MoRDa database updated to version 40 05/01/2021 (DB) ------------------------------------------------------------------------------ ************************************************** MRC image processing programs have moved. You are using image2010 by default. If you wish to use the frozen image2000 you need to : source /public/EM/image2000/com/image.login and source /public/EM/image2000/com/image.cshrc Jude Short (F46 x2039 jms@mrc-lmb.cam.ac.uk) 09.03.2011 ************************************************** Path to mpiexec: /public/EM/OpenMPI/openmpi-2.0.1/build/bin/mpiexec Path to relion_refine_mpi: /lmb/home/tnakane/prog/relion-devel-lmb/build-test/bin/relion_refine_mpi Libraries for relion_refine_mpi: linux-vdso.so.1 => (0x00007ffc2052f000) libcufft.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcufft.so.9.0 (0x00002b9091c9d000) libmpi.so.20 => /public/EM/OpenMPI/openmpi-2.0.1/build/lib/libmpi.so.20 (0x00002b9099d3e000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b909a01d000) libtiff.so.5 => /lib64/libtiff.so.5 (0x00002b909a221000) libfftw3.so.3 => /lmb/home/tnakane/prog/relion-devel-lmb/external/fftw/lib/libfftw3.so.3 (0x00002b909a495000) libfftw3f.so.3 => /lmb/home/tnakane/prog/relion-devel-lmb/external/fftw/lib/libfftw3f.so.3 (0x00002b909a814000) libcurand.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcurand.so.9.0 (0x00002b909ac1f000) libpng15.so.15 => /lib64/libpng15.so.15 (0x00002b909eb83000) libcudart.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcudart.so.9.0 (0x00002b909edae000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00002b909f01b000) libm.so.6 => /lib64/libm.so.6 (0x00002b909f323000) libgomp.so.1 => /lib64/libgomp.so.1 (0x00002b909f625000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b909f84b000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b909fa61000) libc.so.6 => /lib64/libc.so.6 (0x00002b909fc7d000) librt.so.1 => /lib64/librt.so.1 (0x00002b90a004a000) libopen-rte.so.20 => /net/nfs1/public/EM/OpenMPI/openmpi-2.0.1/build/lib/libopen-rte.so.20 (0x00002b90a0252000) libopen-pal.so.20 => /net/nfs1/public/EM/OpenMPI/openmpi-2.0.1/build/lib/libopen-pal.so.20 (0x00002b90a04d1000) libutil.so.1 => /lib64/libutil.so.1 (0x00002b90a07b7000) /lib64/ld-linux-x86-64.so.2 (0x00002b9091a79000) libjbig.so.2.0 => /lib64/libjbig.so.2.0 (0x00002b90a09ba000) libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00002b90a0bc6000) libz.so.1 => /lib64/libz.so.1 (0x00002b90a0e1b000) RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE = /public/EM/SIDESPLITTER/sidesplitter_wrapper.sh SIDESPLITTER = /public/EM/SIDESPLITTER/sidesplitter RUN STARTED AT 1613764248 ----------------------------------------------------------- Reading in optimiser.star ... + Reading in mask ... + The subtracted particles will be re-centred on projections of 3D-coordinate: (14.3241 , -56.4481 , 16.9611) + Calculating Fourier transforms of the maps ... + Subtracting all particles ... 000/??? sec ~~(,_,"> [oo] 0.45/54.02 min ~~(,_,"> 0.88/53.02 min ~~(,_,"> 1.33/53.35 min .~~(,_,"> 1.75/52.52 min .~~(,_,"> 2.22/53.22 min ..~~(,_,"> 2.65/53.02 min ..~~(,_,"> 3.10/53.17 min ...~~(,_,"> 3.52/52.77 min ...~~(,_,"> 4.00/53.35 min ....~~(,_,"> 4.47/53.62 min ....~~(,_,"> 4.93/53.83 min .....~~(,_,"> 5.40/54.02 min .....~~(,_,"> 5.87/54.18 min ......~~(,_,"> 6.35/54.45 min ......~~(,_,"> 6.82/54.55 min .......~~(,_,"> 7.28/54.65 min .......~~(,_,"> 7.73/54.62 min ........~~(,_,"> 8.18/54.58 min ........~~(,_,"> 8.63/54.55 min .........~~(,_,"> 9.12/54.72 min .........~~(,_,"> 9.57/54.68 min ..........~~(,_,"> 10.00/54.57 min ..........~~(,_,"> 10.45/54.55 min ...........~~(,_,"> 10.90/54.52 min ...........~~(,_,"> 11.33/54.42 min ............~~(,_,"> 11.83/54.63 min ............~~(,_,"> 12.32/54.77 min .............~~(,_,"> 12.78/54.80 min .............~~(,_,"> 13.32/55.13 min ..............~~(,_,"> 13.92/55.68 min ..............~~(,_,"> 14.47/56.02 min ...............~~(,_,"> 15.07/56.52 min ...............~~(,_,"> 15.65/56.93 min ................~~(,_,"> 16.20/57.20 min ................~~(,_,"> 16.78/57.57 min .................~~(,_,"> 17.32/57.75 min .................~~(,_,"> 17.85/57.92 min ..................~~(,_,"> 18.38/58.08 min ..................~~(,_,"> 18.93/58.28 min ...................~~(,_,"> 19.48/58.47 min ...................~~(,_,"> 20.00/58.57 min ....................~~(,_,"> 20.55/58.73 min ....................~~(,_,"> 21.10/58.90 min .....................~~(,_,"> 21.65/59.07 min .....................~~(,_,"> 22.20/59.22 min ......................~~(,_,"> 22.72/59.28 min ......................~~(,_,"> 23.25/59.38 min .......................~~(,_,"> 23.78/59.48 min .......................~~(,_,"> 24.32/59.58 min ........................~~(,_,"> 24.85/59.67 min ........................~~(,_,"> 25.40/59.78 min .........................~~(,_,"> 25.98/59.98 min .........................~~(,_,"> 0.44/1.00 hrs ..........................~~(,_,"> 0.45/1.00 hrs ..........................~~(,_,"> 0.46/1.00 hrs ...........................~~(,_,"> 0.47/1.01 hrs ...........................~~(,_,"> 0.48/1.01 hrs ............................~~(,_,"> 0.49/1.02 hrs ............................~~(,_,"> 0.50/1.02 hrs .............................~~(,_,"> 0.51/1.02 hrs .............................~~(,_,"> 0.52/1.02 hrs ..............................~~(,_,"> 0.53/1.03 hrs ..............................~~(,_,"> 0.54/1.03 hrs ...............................~~(,_,"> 0.55/1.03 hrs ...............................~~(,_,"> 0.56/1.03 hrs ................................~~(,_,"> 0.57/1.03 hrs ................................~~(,_,"> 0.58/1.03 hrs .................................~~(,_,"> 0.59/1.03 hrs .................................~~(,_,"> 0.60/1.04 hrs ..................................~~(,_,"> 0.60/1.04 hrs ..................................~~(,_,"> 0.61/1.04 hrs ...................................~~(,_,"> 0.62/1.04 hrs ...................................~~(,_,"> 0.63/1.04 hrs ....................................~~(,_,"> 0.64/1.04 hrs ....................................~~(,_,"> 0.65/1.05 hrs .....................................~~(,_,"> 0.66/1.05 hrs .....................................~~(,_,"> 0.67/1.05 hrs ......................................~~(,_,"> 0.68/1.05 hrs ......................................~~(,_,"> 0.69/1.05 hrs .......................................~~(,_,"> 0.70/1.06 hrs .......................................~~(,_,"> 0.71/1.06 hrs ........................................~~(,_,"> 0.72/1.06 hrs ........................................~~(,_,"> 0.73/1.06 hrs .........................................~~(,_,"> 0.75/1.06 hrs .........................................~~(,_,"> 0.75/1.07 hrs ..........................................~~(,_,"> 0.76/1.07 hrs ..........................................~~(,_,"> 0.77/1.07 hrs ...........................................~~(,_,"> 0.78/1.07 hrs ...........................................~~(,_,"> 0.79/1.07 hrs ............................................~~(,_,"> 0.80/1.07 hrs ............................................~~(,_,"> 0.81/1.07 hrs .............................................~~(,_,"> 0.82/1.07 hrs .............................................~~(,_,"> 0.83/1.07 hrs ..............................................~~(,_,"> 0.84/1.07 hrs ..............................................~~(,_,"> 0.85/1.08 hrs ...............................................~~(,_,"> 0.86/1.08 hrs ...............................................~~(,_,"> 0.87/1.08 hrs ................................................~~(,_,"> 0.88/1.08 hrs ................................................~~(,_,"> 0.89/1.08 hrs .................................................~~(,_,"> 0.90/1.08 hrs .................................................~~(,_,"> 0.91/1.08 hrs ..................................................~~(,_,"> 0.92/1.09 hrs ..................................................~~(,_,"> 0.93/1.09 hrs ...................................................~~(,_,"> 0.94/1.09 hrs ...................................................~~(,_,"> 0.95/1.09 hrs ....................................................~~(,_,"> 0.96/1.09 hrs ....................................................~~(,_,"> 0.97/1.09 hrs .....................................................~~(,_,"> 0.98/1.09 hrs .....................................................~~(,_,"> 0.99/1.09 hrs ......................................................~~(,_,"> 1.00/1.09 hrs ......................................................~~(,_,"> 1.01/1.09 hrs .......................................................~~(,_,"> 1.02/1.09 hrs .......................................................~~(,_,"> 1.03/1.09 hrs ........................................................~~(,_,"> 1.04/1.10 hrs ........................................................~~(,_,"> 1.05/1.10 hrs .........................................................~~(,_,"> 1.06/1.10 hrs .........................................................~~(,_,"> 1.07/1.10 hrs ..........................................................~~(,_,"> 1.08/1.10 hrs ..........................................................~~(,_,"> 1.09/1.10 hrs ...........................................................~~(,_,"> 1.10/1.10 hrs ...........................................................~~(,_,"> 1.10/1.10 hrs ............................................................~~(,_,"> + Saved STAR file with 403474 subtracted particles in Subtract/job387/particles_subtracted.star ----------------------------------------------------------- RUN FINISHED AT 1613768264 ELAPSED WALL CLOCK TIME: 4016 USER=mwilkin Running epilog script on fmb302.lmb.internal Fri 19 Feb 20:57:44 GMT 2021 Removing files owned by mwilkin on /ssd Finished epilog script